When applying GOHyperG to a series of Locus IDs, the function only reports
the GO ID and the corresponding frequencies. But what most people want to
have, when interpreting the GO results is the corresponding Affy IDS which
map on the different Locus IDs and GO IDS.
Code I use
Locusids<-mget(AffyIDS,env=hgu133aLOCUSID)
/*retrieves the LOCUS LINK IDS from a series of AffyIDS*/
MF<- GOHyperG(Locusids,lib="hgu133a",what="MF")
/*reports the occurring Gene Ontologies, the frequencies and the
hypergeometric p values*/
How can I get a result of the form
1. GO ID, freq (output of GoHyperG)
2. GO ID, LOCUS ID (multiple occurring GO IDs)
3. LOCUS ID, AFFY ID (multiple occurring LOCUS IDs)
I know that there is the function hgu95av2GO2ALLPROBES$"GO:0000166" which
retrieves all the probes mapping on a GO, but still it is not the result.
Ok, one would have to make a for loop and look for the occurring probes in
the sample. But isn't there a better way????
Thanks a lot
Michael Auer